Question

Are there any way to find DMR with the data in TCGA methylation level3?

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6.2 years ago

Makplus T ▴ 100

Hi dear all, after downloaded the illumina 450K methylation chip data from TCGA, I have identified the DMCs with Fisher test for each probe, but I have no idea to identify the DMRs. For example I wanna find out the different methy- regions with 1Kb long. Any tool can do it directly? Could any one share some ideas with me? Thanks a lot

TCGA Methylation 450K DMR • 2.0k views

ADD COMMENT • link updated 6.1 years ago by Kevin Blighe 88k • written 6.2 years ago by Makplus T ▴ 100

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Please see this previous thread: Dmr (Differentially Methylated Regions) Identification Software

ADD REPLY • link 6.2 years ago by Kevin Blighe 88k

score 0 · Answer 1 · 2018-10-28

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6.1 years ago

Kevin Blighe 88k

Take a look at TCGAbiolinks, which provides functionality for this.

Kevin

ADD COMMENT • link 6.1 years ago by Kevin Blighe 88k

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Thanks for your help. I have finally solved this problem, but what I use is the other tool called ChAMP., it can accept the beta value matrix as input. AND for the TCGAbiolinks, I have noticed it have this function, but when I read its code in GitHub, it seems do the same works for DMRs just as for the DMCs. Maybe I have some misunderstand for that, but finally I choose the other tool, and solve my problem. Thanks again.